MCQs on Categories of Ligation Reaction
1 - Question
Ligation is defined as ______________
a) Alignment of only double stranded DNA molecules at the ends and the formation of phosphodiester bonds between both the strands
b) Alignment of either of the double or single stranded DNA molecules and formation of glycosidic bonds between both the strands
c) Alignment of either of the double or single stranded DNA molecules and the formation of phosphodiester bonds. The bond can be between either one or both the strands
d) Alignment of single stranded DNA molecules and formation of glycosidic bonds between these strands
Explanation: Ligation is basically the formation of bonds between the ends of two DNA strands. The strands can be single or double. The nature of the bond is phosphodiester, which means that bond is formed between sugar and phosphate. The phosphodiester bond can either be formed between one strand or both the strands.
2 - Question
If only one bond is broken in the sugar-phosphate backbone, it is called as ___________
Explanation: In the case, if only one bond is broken in the sugar phosphate backbone, it is termed as nick. If a number of nucleotides are missing, it is termed a gap. Nick can be sealed by ligation reactions but gap can’t be sealed by a ligation reaction.
3 - Question
How many categories of ligation reaction are there on the basis of ends created?
Explanation: There are two categories of ligation reaction and are named as blunt-ended and sticky ended reaction. They are named because of the nature of the ends of the molecules to be ligated.
4 - Question
In the case of blunt-end ligation, blunt ends can be generated by ___________
a) simply the action of restriction endonuclease which gives straight ends
b) the polishing of staggered ends
c) both the action of restriction endonuclease which gives straight ends and polishing of staggered ends
d) by the action of restriction endonuclease which gives staggered ends
Explanation: Blunt ends are those which don’t have single stranded ends as overhangs. The ends are double stranded. And these can be generated by polishing the staggered ends or the action of restriction endonuclease which generate straight ends.
5 - Question
The ligation reaction is more efficient in which case?
a) Blunt end ligation
b) Sticky end ligation
c) Both have the same efficiency
d) Depends on the reaction conditions
Explanation: Sticky end ligation is generally more efficient than blunt end ligation. It is so because sticky end ligation is carried out because of complementary base pairing.
6 - Question
The sticky ends are held together by which type of bonds?
a) Hydrogen bond
b) Covalent bond
c) Ionic bond
d) Van-der-waal forces
Explanation: The sticky ends are held together by the hydrogen bonds. Hydrogen bonds are weak in nature and can easily be broken.
7 - Question
Why sticky ended ligations are carried out at temperatures lower than room temperature?
a) It is so because the vibrational and kinetic energy of the molecules at room temperature is lower than that of the energy required to break the bonds holding the ends
b) The energy required to break the bonds holding the ends is very less than that of the kinetic and vibrational energy at room temperature
c) The enzyme carrying out ligation is unstable at low temperature
d) The sticky ends created, don’t just relegate at low temperature
Explanation: The sticky ends are held together by the hydrogen bonds. These hydrogen bonds are weak in nature and the energy required to break them is very less than the kinetic and vibrational energy of the molecules at room temperature. Hence the reaction is carried at 4 degrees.
8 - Question
Ligation reaction can be both intramolecular and intermolecular in nature
Explanation: Ligation reaction can be both intramolecular and intermolecular in nature. The intermolecular reaction is that which ends ligated are of two different molecules. The intramolecular ligation is that which ends ligated belong to the same molecule.
9 - Question
If a ligation reaction is being carried out and recircularization is observed, which type of reaction is being carried out?
c) Both observe recircularization equally
d) Recirculation is not possible in any of the cases
Explanation: Recircularization is the phenomenon of joining the ends of the same molecule. It happens in the case of intramolecular ligation reaction.
10 - Question
What is the kinetics of the intramolecular and intermolecular ligation reactions?
a) Second order kinetics for intramolecular and first order for intermolecular
b) First order kinetics for intramolecular and second order for intermolecular
c) Both are first order
d) Both are second order
Explanation: As the intramolecular reaction requires only the type of reaction species, the reaction is first order.Whereas, on the other hand intermolecular reaction requires collision between two different species and hence it is second order reaction.
11 - Question
What are the effects of increasing concentration of reaction components?
a) It increases chances of ligation in both intramolecular and intermolecular reactions
b) It increases chances of ligation only in intermolecular and no effect on intramolecular
c) It decreases chances of ligation in intramolecular and increases in that of intermolecular
d) It decreases chances of ligation in both types of reaction
Explanation: As the concentration of reaction components is increased, there are increased chances of ligation in intermolecular reaction because of frequency of collision of two different molecules increases. The intramolecular reaction is unaffected because the probability of meeting the ends of a molecule remains the same.